Pokemon Emerald: What really happened
by Spastic Deoxys
Summary: When two twins are forced to move to a new orphanage in Hoenn, they have no idea that soon, their entire life will have changed dramatically.
1. Prologue

Prologue

So? You think you know the story of Pokémon Emerald, eh?

Well, did you find that from the game?

Yes?

Then, everything you know is wrong.

Well, not literally everything, but you've got some major facts mixed up, thanks to Nintendo. They had to keep some stuff out so the kids didn't get scared.

What? You doknow everything?

Okay, then. Where was Rayquaza sleeping? Sky Temple? No. Wrong.

You are still adamant? Okay, then. I bet you didn't know the story kicks off in Johto, did you? I bet you didn't know that the story takes 34 years to finish. And I bet you don't know about Scott's Shadow Agent, or the Blackwing Conspiracy.

And I bet you don't know what Deoxfusis is.

See? I was right.

You're green. You don't know anything.

Good thing I'm here to help.

I know what happened. I was there, watching everything. In fact. I was everything. Well, I was nearly everything, anyway.

So, if you want to know, read on.

Get ready to learn.

Get ready to learn the truth.


	2. Chapter 1: Leaving Johto

Chapter One: Leaving Johto

It was a bright summer afternoon in Azalea Town, the small farming community located on a hill in Eastern Johto. Birds sang merrily in the huge trees. Every community activity was cancelled due to the unusual heat wave, temperatures over 5 degrees Celsius. Everyone was experiencing pure bliss. But something in the orphanage down at Monarch's Road was about to change all that.

The gate was the scariest thing about it. They were big, black, iron things with the Johtonian Emblem on. At this point in time, an old woman was walking along the road, carrying her shopping home. She had a lot in her hands, and was probably old enough to be knocked aside by a feather.

It's always the people who can suffer most who do.

A piercing scream filled the air, covering all of Azlea and the surrounding countryside. The birds flew in the general direction of Cianwood City, people everywhere jumped in shock, and the old lady had a heart attack and had to be carried of to the hospital on the other side of town.

In the third floor of the big, white building – the orphanage - was the Matron's office. It was a huge room in an art deco style, and there was furniture everywhere. In it was the matron, a blonde 50-year-old hag with a literal fist of steel where a Houndoom bit it off, and two 14 year old children. They were twins, and their names were Brendan and Seth Richards They were both wearing exactly the same red and green swimming kits, and were dripping with water, and what seemed to be blood.

"Now, boys. How many times do I have to tell you not to do that to people! I don't want to have to deal with another murder charge!" the matron screamed. To anyone else, the matron would have sounded as stupid as a tree would look in a smelting factory, but these boys knew exactly what she meant.

"It wasn't our fault, Ma'am!" They both cried in unison.

"I don't care what happened! That was the last straw! You are being moved to a new orphanage!"

There was silence.

_please, please, don't let it be in Hoenn!_ The first kid in the room thought.

The matron spoke again.

"You're going to Hoenn, because nowhere else in Johto will take you!"

At that, the boys had a total and utter mental breakdown, which was actually quite funny to see. Seth had an attack of nerves, crawling into a corner and shaking violently, every now and again giving small static-sounding chirps. Brendan started to sob loudly, buckling over and hitting the floor with a thud.

"Boys!" The matron shrieked, "I do not need this! Pack your bags, and at one o' clock, meet me by the front gate! You got half an hour, so get out of my sight!"

Three hours later, at the front gate of the orphanage, after much delay. On the outside, the orphanage looked like a stately home, but on the inside, it had the atmosphere of a hospice. Everyone in the orphanage had been orphaned at a time they were just old enough to remember. Most of the children had parents that had committed suicide. Brendan and Seth's parents were Norman and Winona. They were Gym Leaders.

But they hadn't committed suicide. Oh, no. During a double Pokémon battle skirmish organized in the capital city, Petalburg, they had been assassinated. All the twins dreamt and thought about was the assassination. The sickeningly frightening amount of blood and gore, the injuries when the assassins tried to turn on them, the mistreatment in Petalburg Sector 2 Hospital, and the loneliness after. That, and their disease.

They called it Dexofuzis. Fusing the DNA of something into something else. This was of questionably inaccurate, because that wasn't the case at all. Brendan and Seth literally fed on the life force of other people via skin contact. Slight exposure leaves the victim with a headache and nausea. A couple of minutes contact and the victim will faint. Thirty more seconds and you've got a murder case on your hands. This is bad because a; the twins could sense an aura around people determining the quality and stability of the life force, b; they subconsciously forced themselves to, and c; they had to do so, food being highly toxic to the twins, and only being able to get nutrients e.t.c. from peoples life force and nectar (from flowers.) In view of that, it's surprising they had only changed orphanages twice in 8 years!

At the front gate of the orphanage was a large crowd of people. One of them was Brendan's friend, twelve were standing by the front gate so they didn't have to move far to get to the party for the twins leaving, and the other fifty-seven were in the middle of the road following a funeral procession of an 83-year-old woman who had suffered a heart attack whilst coming home from Tesco's. Brendan trudged down the road, followed by Seth.

"Hey! Wait! A kid in the crowd called. Seth turned round, and the kid threw a small envelope in the air. Now, that wasn't a very good idea, because at the time there was a lot of wind. So, Seth jumped to catch it, but it was way out of reach, and whizzed in the direction of the funeral procession. Seth's eyes glowed an intense flaring red. Brendan, who was walking towards the coach, stopped mid-walk, his eyes glowing a bright, vibrant, yet natural green. Seth jumped into the air, the jump flipping him high enough to jump a three-storey building, and landed hands-first on Brendan's shoulders, only to then subsequently launch himself into the air. Brendan followed suit, and, after launching another thirty feet into the air, zoomed straight for the funeral procession. At this time, the letter was just above the coffin, so he grabbed the letter and pocketed it, stopped from only falling into the final resting place of the OAP by Seth, who at that moment had just teleported 6 meters and supported himself in mid-air by a well-known Pokemon move - Teleport.

Vzshhhhhhhhhhhhhhhhhukup! The twins disappeared and rematerialized next to the coach. Oblivious to the people staring at them, they got in.

Inside the coach wasn't very well organized. People were smoking, flicking chewing gum, screaming, and acting rowdily. Seth chose a seat away from the other people, and Seth managed to stay still for exactly two seconds before the nagging sense of curiosity in his brain overpowered him. "What's in the letter?" He asked, rather anxiously.

"I was just about to look." Brendan opened the envelope. In it was a large green crystal with a leaf emblem engraved on the stone, a red crystal which looked as if someone had cut its top open, filled it with red, orange and yellow liquids and then perfectly re-sealed it, two telescopic poles, and a letter.

"What does it say? What does it say?"

"It says:

Sorry about that incident. I know you didn't mean to do that (But it did hurt!) Matron said it took an entire hour to get me to move. But, unlike the matron, I don't blame you. Anyway, I watched that fight you two had against those thugs, and recorded it on my PokeDex. You both used Pokémon moves you can't learn from TMs - Natural moves! So, I was thinking. If you can use Pokémon moves, you could evolve like Pokémon, too! (Hence the evolutionary stones in the envelope.)

P.S. I am still your friend. If you need to contact me, I have a vid phone with a call number of - 140.2 - 1195 if you need anything hacked into, just give me a call!

P.P.S. This is just a theory. It probably won't work. I know it's stupid, but, that's what they said Galileo was. (Not sure if it was Galileo, Newton or Einstein.)

P.P.P.S. Above, I meant the main part of the theory. Not the first post script.

P.P.P.P.S. Sorry for all the Post Scripts.

P.P.P.P.P.S. including that one.

P.P.P.P.P.P.S. Etcetera, etcetera...

P.P.P.P.P.P.P.S. Post Scripts, hacking, Espeon and Porygon Z rock!

P.P.P.P.P.P.P.P.S. I'm going over the top, here…

P.P.P.P.P.P.P.P.P.S. The poles are yours. You left them in the dormitory.

Best Friend:

Samuel Helmsmith

As Brendan finished the letter, he took out the two stones. He handed Seth the green stone, green being his favorite colour.

"Do you know how to use evolutionary stones?" He asked.

"I thought you did." Was the reply.

"Well, let's just pocket them." Seth didn't pocket his stone. Instead, he clenched it in his fist. It felt warm and smooth. Another sense of curiosity emerged five seconds after the first one just died down, and, wondering where they had gone past, looked out of the window. They were crossing through Violet Town - a well known port town. Even from the cab, he could smell the sea. He felt tired and light-headed, and soon, he fell asleep. But he didn't dream. He consciously started changing the signals of his brainwaves. Brendan picked these up and read them. Brendan then sent another signal, which Seth read. Simply put, they could communicate telepathically. (One side-effect of Deoxfusis unknown to scientists, and one of the better ones.) Brendan could channel or receive these brainwaves no matter what he was doing, but Seth could only receive thoughts whilst sleeping.

/Are we there yet/ Seth asked.

/No. Why don't you wake up and take a look for yourselves?/ Brendan said, irritated. He had been trying to relax for the past hour, but to no avail. There was a tight knot in his stomach, being pulled apart by memories he didn't want to even remember about remembering.

/I'm too tired to wake up. /

/Oh. /

/Can you actually speak any Hoenian/ Seth asked, only tightening the knot in Brendan's stomach.

/Yes. /

/You're better than me. I only know my name... Seru…/ Seth said. He sounded like he didn't even want to know that.

/Whoa. You really wanted to forget Hoenn, didn't you/

/To me, Hoenn is just the perfect island covered in blood and dark memories. Making it _not_ the perfect island. What are your memories of Hoenn/

That exploded Brendan's subconscious. Two loud gunshots. Blood spurting from his parents' bleeding foreheads, turning around, a flash of light, and what seemed like eternal pain. He started crying.

/Don't worry. Stuff like that shouldn't happen. /

/How are you sure/ He asked.

/I'm not. But all I know is that things are going to have to get better.../


	3. Chapter 2: SS Cactus

Chapter Two: S.S. Cactus

Seth woke up half-way across the Joho Sea, on the ferry. He had obviously been carried on whilst he was sleeping. He opened his hand to pick the leaf stone up and stare at it. But it wasn't there. Seth ignored this and immediately dozed off, just to be woken up again by a loud slam of a door somewhere in the room. He yawned.

"Who is it?" He asked, in his Azalean accent. Azalea, although legally a town, is very big, and there are two almost unintelligible accents, one for north Azlea, and one for South. The south accent has lots of vowel slurring, fast consonants, and is considered one of the seven most unintelligible accents in the United Regions (UR).

"Seth. It's me. Brendan." His twin replied, in a similar accent.

"What are you two saying?" Another voice asked. It was a male, higher-pitched, weaker one. "Not wanting to offend you or anything, but, I can't understand your funny accent." the voice started coughing. Seth opened his eyes. Brendan was sitting down on a small chair, playing on a handheld video games console he had received from his Kantonese uncle a month ago. There was also another child, with green hair and eyes. He was wearing a shirt, formal trousers, boots, and gloves, all in a shade of green. A small Shroomish was sitting on the top of his head, sleeping.

"Oh, sorry. What's your name?" Seth replied, straightening his accent."

"My name's Wally." Wally replied.

"So. Why are you here?" Seth asked. Wally sat down, and started talking. The only problem was that he was speaking in a different language. "Damn" The kid had started talking in Kantonese, and had only stopped when he had noticed, which, given the length of the language, was quite a long time.

"Damn!" Wally shouted, nearly waking up the Shroomish.

"Do you come from Kanto?" Seth asked.

"No. I come from Hoenn. My dad is very important, and in order to get _anything_ across to people I have to learn their language. I know Kantonese, Johtonian, Hoenian, and Japanese. When you get past the grips of the words, numbering system, and that they write backwards, Kantonese is actually a very easy language to communicate in. And, I was just in Kanto, talking to Red." The twins gasped in shock at this. To know the World Champion, you need to have a team of powerful Pokémon, or be very important.

"You know Red?"

"Yep."

"Are your parents' gym leaders?" Brendan asked.

"Yeah." At that moment, there ship turned violently, and everyone and everything that wasn't bolted down went flying. Inside the cabin Brendan, Seth, and Wally were in, everything went flying into the starboard wall with a sickening snap.

"Oww... My head..." Brendan groaned in agony. He had been thrown upside-down into a corner of a room and now looked like a large rag-doll, mauled by a rabid dog. Seth had been flung down from the top bunk of the bed he had been in, into a large antique mahogany table, which had subsequently snapped in half. Wally had been thrown straight into the door, his head snapping through the door, the rest of his body stuck on the other side. The back of his shirt had been mauled, and jutting out of his back, was a long, immaculate, black-feathered wing. Wally felt the area around his back, and found the wing.

There was only silence, broken briefly by a loud "Shroo!" from underneath the bed.

"Erm..." He stuttered nervously, "C-can you two keep Chapter Two: Gym Leader Offspring

Seth woke up half-way across the Joho Sea, on the ferry. He had obviously been carried on whilst he was sleeping. He opened his hand to pick the leaf stone up and stare at it. But it wasn't there. Seth ignored this and immediately dozed off, just to be woken up again by a loud slam of a door somewhere in the room. He yawned.

"Who is it?" He asked, in his Azalean accent. Azalea, although legally a town, is very big, and there are two almost unintelligible accents, one for north Azlea, and one for South. The south accent has lots of vowel slurring, fast consonants, and is considered one of the seven most unintelligible accents in the United Regions (UR).

"Seth. It's me. Brendan." His twin replied, in a similar accent.

"What are you two saying?" Another voice asked. It was a male, higher-pitched, weaker one. "Not wanting to offend you or anything, but, I can't understand your funny accent." the voice started coughing. Seth opened his eyes. Brendan was sitting down on a small chair, playing on a handheld video games console he had received from his Kantonese uncle a month ago. There was also another child, with green hair and eyes. He was wearing a shirt, formal trousers, boots, and gloves, all in a shade of green. A small Shroomish was sitting on the top of his head, sleeping.

"Oh, sorry. What's your name?" Seth replied, straightening his accent."

"My name's Wally." Wally replied.

"So. Why are you here?" Seth asked. Wally sat down, and started talking. The only problem was that he was speaking in a different language. "Damn" The kid had started talking in Kantonese, and had only stopped when he had noticed, which, given the length of the language, was quite a long time.

"Damn!" Wally shouted, nearly waking up the Shroomish.

"Do you come from Kanto?" Seth asked.

"No. I come from Hoenn. My dad is very important, and in order to get _anything_ across to people I have to learn their language. I know Kantonese, Johtonian, Hoenian, and Japanese. When you get past the grips of the words, numbering system, and that they write backwards, Kantonese is actually a very easy language to communicate in. And, I was just in Kanto, talking to Red." The twins gasped in shock at this. To know the World Champion, you need to have a team of powerful Pokémon, or be very important.

"You know Red?"

"Yep."

"Are your parents' gym leaders?" Brendan asked.

"Yeah." At that moment, there ship turned violently, and everyone and everything that wasn't bolted down went flying. Inside the cabin Brendan, Seth, and Wally were in, everything went flying into the starboard wall with a sickening snap.

"Oww... My head..." Brendan groaned in agony. He had been thrown upside-down into a corner of a room and now looked like a large rag-doll, mauled by a rabid dog. Seth had been flung down from the top bunk of the bed he had been in, into a large antique mahogany table, which had subsequently snapped in half. Wally had been thrown straight into the door, his head snapping through the door, the rest of his body stuck on the other side. The back of his shirt had been mauled, and jutting out of his back, was a long, immaculate, black-feathered wing. Wally felt the area around his back, and found the wing.

There was only silence, broken briefly by a loud "Shra secret?

"Okay." Brendan said, for the umpteenth time. "Can you explain that again?"

Wally sighed, grabbed the only chair in the room that hadn't been smashed, sat down, and started explaining again, his wing flopping loosely from his shoulder blade. "My dad is a gym leader. Before they had been in the E4, they worked at the Goldenrod Medical Laboratory. They had been studying about a new type of radiation. They had tested Pokémon, insects, viruses, but they needed a human for testing as well. At that time, I was five years old. My dad sold me over to them. They stuck this thing on my head, and everything went black. When I woke up, the pain..." Wally stopped, as if suppressing what he was just about to say, "Anyway... Right now, me and Mushy are more or less fleeing from him."

"Mushy?" Brendan asked.

"Mushy. The Shroomish." Wally pointed in the direction of a corner, where the Shroomish was trying to eat a wall, its own small black wing hanging loosely out from its' spore hole. "He's my avatar."

"Avatar?" Seth asked.

"Yeah. I'm from a Gym Leader's family. Of course I have an avatar. It's natural. Just like I can use Pokémon moves, and I can summon a huge sword like that." He boasted, clicking his fingers in emphasis.

/How come we don't have avatars?/ Brendan asked his brother.

/I don't know. We can use Pokémon moves, though…/

/Yeah, but we can't summon weapons…/

/Why should we care?/

/I don't know, but we should./ Seth stated, with no reply, only a blank stare.

Wally continued what he was saying. "He treats me like I'm nothing! As if I'm nothing but a plague rat!" Wally's skin started glowing, a dark green, with Unowic runes flashing across his face every now and then.

"Umm..." Seth said, looking for a way out of the conversation. He was feeling hungry and tired.

'Aha!' He thought. The perfect way out!'

"I'm just going downstairs. I haven't had anything to eat for ages!" Seth knew very well he couldn't eat actual food, but both the twins knew what he really meant. As what he had said was true. He hadn't eaten for ages. But, that depends how you class the word 'eating.'

"Don't!" Brendan shouted, but Seth was almost halfway down the corridor outside the cabin, and even if he did hear, it wouldn't work.

"Wally." Brendan said, his voice strained. Can you run fast?

"Um... yes. Why?" Wally asked.

"Hmmm..." Brendan paused. "Let's just say that the lives of about 300 people are at stake."

Seth sprinted down the corridor, not caring where he was going. He turned a left, then a right, then another left. He was in a large, open room being used as a disco hall. There were people everywhere, singing, dancing, and shouting, talking, drinking and working. He spotted someone go out of the room. He followed her. She walked down the stairs, and stopped to look out a window. Seth seized his chance, and jumped. He kicked her down the steps, and sprinted down. By the time he had got to the bottom of the stair, the woman had got up, and ran towards him back up the stair. The woman's fist connected with the railing as he tried to punch Seth. Seth grabbed the person's wrist, and smiled, licking his lips.

Brendan jumped down the steps, six at a time, Wally following close behind. They were about to turn left, when they heard a scream.

"Oh, no." Brendan turned his head the other way. Seth was down there.

Wally ran down the corridor and charged, Misty hanging onto his hair. Brendan followed. When they got to the end of the corridor, the woman had gone. Seth, however, was standing there, his eyes just green lights. Literally. His entire eye had turned green.

'Bloodlust. Damn!' Brendan thought.

"Wally?" Brendan asked.

"Yes?" Was the reply.

"Run back the way you came, hold on to something strong, and cover your ears." There was a sense of urgency in Brendan's voice, so Wally ran.

Brendan turned again, and braced himself.

Wally had just reached the top floor when it hit him. A howl that had smashed the windows on the deck and threw people overboard. Wally would have been one of them if he hadn't been clutching the rail in exhaustion, the rail that was now shaken off his hinges. He quickly scooped Misty off of the ground and into his arms, and relaxed slightly.

_bleep_

That bleep sounded like an intercom. The bleep had come from around the wall. Wally listened in on the conversation curiously.

"...Giovanni? Yeah. I got what you're looking for. He's here." This voice was female, and stubborn.

"Good. Execute protocol five-one-three." The intercom crackled.

"Boss! Boss! I've got some more news!" This voice was male, slightly older, and chirpy. "There are two of them! Heading for Petalburg City! They're twins! And another one, a sort of mutant with a wing-"

_Mutant with a wing?_ That angered Wally so much; it took all his strength to not charge at the two adults round the corner.

"Two of them?" The 'boss' asked, "This is better than I thought."

"And, there's something else!" The man chirped in. "I've - Meowth! Stop that!"

"I WANT TO SEE! I WANT TO SEE!" Another voice cried. It sounded like a Pokémon, however. There was a _tssssssssssss_ing sound, and the Pokémon started snarling madly, probably due to being hit with a can of repel spray.

"Okay." The intercom crackled. "Get to work, and you might finally get recruited to Super Rank Orion. Catching them would put you at a higher level that anyone else in the organization, except from me."

"Got it."

Wally turned the corner and powerwalked back down the stairs. It had sounded like those two people were talking about Brendan and Seth, so, quite rightly, he had to alert them. He had just walked a step down when a tugging, clawing sensation hit him. There was a burning sound, and then whatever was on him jumped a mile. Wally, ignoring the fact his skin was glowing again, turned back. A Meowth, fur burnt, was skulking up the steps.

"A Meowth? What's it doing on the S.S. Cactus?" Wally asked himself, before hightailing it down the stairs.

Brendan jumped over the overturned flower-pot and continued running. His brother had long exited this corridor, but it was easy to see where he had been. There was destruction and carnage, in a long line up to the deck. He finally reached the top deck, and went smack-bang into a big sign that read: Swimming Pool.

"Swimming Pool... Damn!" Brendan cursed, realizing what was going to happen if he didn't act fast.


End file.
